MIP1 DNA-directed DNA polymerase gamma MIP1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: MIP1
Gene description: DNA-directed DNA polymerase gamma MIP1
Primary source: SGD:S000005857
Locus tag: YOR330C
See related: AllianceGenome:SGD:S000005857
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables 3'-5' exonuclease activity and DNA-directed DNA polymerase activity. Involved in mitochondrial DNA catabolic process and mitochondrial DNA replication. Located in mitochondrion. Used to study Alpers-Huttenlocher syndrome; chronic progressive external ophthalmoplegia; peripheral nervous system disease; and progeria. Human ortholog(s) of this gene implicated in several diseases, including mitochondrial DNA depletion syndrome (multiple); mitochondrial myopathy (multiple); neurodegenerative disease (multiple); ovarian disease (multiple); and sensory ataxic neuropathy, dysarthria, and ophthalmoparesis. Orthologous to human POLG (DNA polymerase gamma, catalytic subunit). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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Location:: chromosome: XV

Exon count:: 1

Sequence:: Chromosome: XV; NC_001147.6 (939621..943385, complement)

Chromosome XV - NC_001147.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001147.6

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

N-terminal deletions in Mip1 polymerases abolish polymerization and decrease exonucleolytic degradation, whereas moderate C-terminal deletions reduce polymerization. Similarly, to the N-terminal deletions, an extended C-terminal deletion of 298 amino acids is deficient in nucleotide addition and exonucleolytic degradation of double and single-stranded DNA.
Title: Amino and carboxy-terminal extensions of yeast mitochondrial DNA polymerase assemble both the polymerization and exonuclease active sites.
Herein the authors found that Rpo41 transcribes RNAs that can be extended by Mip1 on single and double-stranded DNA.
Title: Yeast mitochondrial RNA polymerase primes mitochondrial DNA polymerase at origins of replication and promoter sequences.
Our study also further confirms the utility of yeast Mip1p as a tool for studying human DNA polymerase (pol gamma)variants.
Title: Yeast model analysis of novel polymerase gamma variants found in patients with autosomal recessive mitochondrial disease.
Disrupting exonuclease activity of mutant variants was not associated with increased spontaneous mutagenesis compared with exonuclease-proficient alleles, suggesting that most or all of the mtDNA was replicated by wild type Mip1.
Title: MMS exposure promotes increased MtDNA mutagenesis in the presence of replication-defective disease-associated DNA polymerase γ variants.
Yeast Mip1, the mitochondrial DNA polymerase gamma, harbors a conserved C-terminal extension required for maintenance of mitochondrial DNA in vivo.
Title: The carboxyl-terminal extension on fungal mitochondrial DNA polymerases: identification of a critical region of the enzyme from Saccharomyces cerevisiae.
disruption of Mip1 exonuclease activity increases mtDNA deletions 160-fold.
Title: The exonuclease activity of the yeast mitochondrial DNA polymerase γ suppresses mitochondrial DNA deletions between short direct repeats in Saccharomyces cerevisiae.
Point mutations in the 3'-5' exonuclease domain of Mip1 result in severe impairment of the polymerase function and DNA binding.
Title: A cluster of pathogenic mutations in the 3'-5' exonuclease domain of DNA polymerase gamma defines a novel module coupling DNA synthesis and degradation.
mip1 containing mutations associated with mitochondrial disease causes mutagenesis and depletion of mtDNA in Saccharomyces cerevisiae.
Title: mip1 containing mutations associated with mitochondrial disease causes mutagenesis and depletion of mtDNA in Saccharomyces cerevisiae.
Mip1p contains a single nucleotide polymorphism changing the strictly conserved threonine 661 to alanine. This substitution is responsible for the increased rate of mitochondrial DNA point mutations and deletions in these strains.
Title: A single nucleotide polymorphism in the DNA polymerase gamma gene of Saccharomyces cerevisiae laboratory strains is responsible for increased mitochondrial DNA mutability.
The yeast mitochondrial DNA (mtDNA) replicase Mip1 has been used as a model to generate five mutations equivalent to POLG mutations associated with a broad spectrum of diseases in human.
Title: Mitochondrial DNA defects in Saccharomyces cerevisiae caused by functional interactions between DNA polymerase gamma mutations associated with disease in human.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables 3'-5' exonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables 3'-5' exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-directed DNA polymerase activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-directed DNA polymerase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-directed DNA polymerase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in mitochondrial DNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrial DNA replication	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitochondrial DNA replication	IDA Inferred from Direct Assay more info	PubMed
involved_in mitochondrial DNA replication	IEA Inferred from Electronic Annotation more info
involved_in mitochondrial DNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrial genome maintenance	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of gamma DNA polymerase complex	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	HDA more info	PubMed
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: DNA-directed DNA polymerase gamma MIP1

NP_014975.2

EC 2.7.7.7

Mitochondrial DNA polymerase gamma; single subunit of mitochondrial DNA polymerase in yeast, in contrast to metazoan complex of catalytic and accessory subunits; polymorphic in yeast, petites occur more frequently in some lab strains; human ortholog POLG complements yeast mip1 mutant; mutations in human POLG associated with Alpers-Huttenlocher syndrome (AHS), progressive external ophthalmoplegia (PEO), parkinsonism, other mitochondrial diseases

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001147.6 Reference assembly

Range

939621..943385 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183750.1 → NP_014975.2 TPA: DNA-directed DNA polymerase gamma MIP1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014975.2

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W327, P15801, Q08785

UniProtKB/TrEMBL

A0A8H4BW69, B3LJZ1

Conserved Domains (2) summary

cd08641
Location:581 → 960

DNA_pol_gammaA; Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria

pfam18136
Location:95 → 362

DNApol_Exo; DNA mitochondrial polymerase exonuclease domain